I'm trying to get 5.2 V @ 1.3 A to power my system, using two of your Adafruit 4.2 V 2500 mAh batteries in parallel, with your Adafruit Powerboost 1000 Basic schematic in the systems PCB. The problem is that the power booster seems to only be able to supply that needed current when the batteries are above 3.7 V. This inevitably makes my system die and cut-out early at 3.7 V battery life, rather than at 3 V when the battery dies.

In the photo file attached you will see my schematic, which reflects the Adafruit Powerboost 500 Basic. In reality chips have been replaced to match your Adafruit Powerboost 1000 Basic, rather than your Adafruit Powerboost 500 Basic. It looked like to me that the only difference in the schematics, is R4 340 KOhm resistor is replaced with a 200 KOhm resistor, and C6 100uF capacitor is replaced with a 220uF capacitor. Is what I'm trying to do possible with the power booster and batteries given? What do I need to change to make this possible? Or should it be working just fine and I need to actually redo my entire PCB?